水分ライソ酵素で水回転のリラックスと拡散

Massimo Marchi¹, Fabio Sterpone, Matteo Ceccarelli

¹Commissariat à l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Etudes, Saclay, 91191 Gif-sur-Yvette Cedex, France. marchi@villon.saclay.cea.fr

Journal of the American Chemical Society

|June 6, 2002

まとめ

タンパク質の近くの水の動態は著しく減速する. 分子動力学シミュレーションでは,表面水の拡散とリラックスが散水と比較して遅れていることが示され,核磁気リラックス分散研究に影響を与えています.

科学分野:

バイオフィジックス生物物理学
物理化学物理化学
コンピュータ生物学コンピュータ生物学

背景:

タンパク質と水分化殻の相互作用を理解することは,生物学的プロセスにとって極めて重要です.
タンパク質表面の近くの水のダイナミクスは,散布水と異なる.
核磁気リラックス分散 (NMRD) 研究は,水の動力学に関する仮定に依存しています.

研究の目的:

球状タンパク質 (リゾ酵素) の周辺の水分子のダイナミクスを調査する.
表面水の二極二次リラクゼーション時間と拡散特性を計算する.
シミュレーション結果をNMRDの推定値と比較し,異なる水モデルを評価する.

主な方法:

水中のリゾ酵素の広範な分子動力学 (MD) シミュレーション.
合計シミュレーション時間は28ナノ秒.
水分子の回転リラクゼーションとトランスレーション拡散特性の計算.

主要な成果:

ライソジームの近くの水の回転のリラックス化は,散発水よりも3〜7倍遅い.
ライソジームの近くの水の翻訳的拡散は,同様の遅延を示しています.
表面水は分散的拡散またはサブ拡散のダイナミクスを示します.
計算されたリラックス時間とNMRDの推定値との間の良好な一致が達成されました.

結論:

タンパク質の表面水の動態は,散布水よりも著しく遅い.
MDシミュレーションは,NMRD研究に関連する水のダイナミクスに関する貴重な洞察を提供します.
SPC/Eの水モデルでは,TIP3Pと比較して,リゾジームを取り巻く水動力のより現実的な記述を提供している.

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